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GEOCHEM–EZ is a multi-purpose chemical speciation program, designed to replace Geochem-PC, which can only be used in DOS consoles. This program is used in plant nutrition to perform equilibrium speciation computations to estimate the activity of ions in solution and to consider simple complexes and solid phases. It is also important in molecular biological research to modify solution composition for phenotyping and screening transformed organisms (e.g., transgenic Arabidopsis plants), controlling pH, redox conditions, ionic strength (e.g., for protoplast isolations) or for using heterologous systems, such as yeast expressing plant genes.To enhance the usability and to address several weaknesses of Geochem-PC, we upgraded the program using a Java graphical user interface, improving both the power and function, and allowing it to run on any computer that supports Windows XP, Vista, or Windows 7.This program includes improvements, such as interactive and illustrated help files, hierarchical organization of options, logical output, and real-time error checking, while maintaining complete backward compatibility to the Geochem-PC format. We added a customizable database of common salts, eliminating the need to parse and calculate the concentration of each metal or ligand. This last feature will make data input more rapid and help eliminate the most common user errors. One can instantly preview input and output files and make necessary corrections (e.g. charge balance the solution), something that formerly involved having to save these files and run the calculations a second time. GEOCHEM-EZ is available as a free download from http://www.plantmineralnutrition.net/Geochem/geochem%20home.htm

Root system architecture (RSA) plays an important role in the acquisition of both nitrogen (N) and phosphorus (P) from the environment. Currently RSA is rarely considered as criteria for selection to improve nutrient uptake efficiency in crop breeding. Under field conditions roots can be greatly influenced by uncontrolled environment factors. Therefore, it is necessary to develop fast selection methods for evaluating root traits of young seedlings in the lab which can then be related to high nutrient efficiency of adult plants in the field. Here, a maize recombination inbred line (RILs) population was used to compare the genetic relationship between RSA and nitrogen and phosphorous efficiency traits. The phenotypes of eight RSA-related traits were evaluated in young seedlings using three different growth systems (i.e., paper roll, hydroponics and vermiculite), and then subjected to correlation analysis with N efficiency and P efficiency related traits measured under field conditions. Quantitative trait loci (QTL) of RSA were determined and QTL co-localizations across different growth systems were further analyzed. Phenotypic associations were observed for most of RSA traits among all three culture systems. RSA-related traits in hydroponics and vermiculite weakly correlated with Nitrogen (NupE) uptake efficiency (r = 0.17-0.31) and Phosphorus (PupE) uptake efficiency (r = 0.22-0.34). This correlation was not found in the paper roll growth system. A total of 14 QTLs for RSA were identified in paper rolls, 18 in hydroponics, and 14 in vermiculite. Co-localization of QTLs for RSA traits were identified in six chromosome regions of bin 1.04/1.05, 1.06, 2.04/2.05, 3.04, 4.05, and 5.04/5.05. The results suggest the problem of using the phenotype from one growth system to predict those in another growth system. Assessing RSA traits at the seedling stage using either hydroponics or a vermiculite system appears better suited than the paper roll system as an important index to accelerate the selection of high N and P efficient genotypes for maize breeding programs. [ABSTRACT FROM AUTHOR]

Aluminum (Al) toxicity inhibits root growth and limits crop yields on acid soils worldwide. However, quantitative information is scarce on protein expression profiles under Al stress in crops. In this study, we report on the identification of potential Al responsive proteins from root tips of Al sensitive BR007 and Al tolerant SC566 sorghum lines using a strategy employing iTRAQ and 2D-liquid chromatography (LC) coupled to MS/MS (2D-LC-MS/MS). A total of 771 and 329 unique proteins with abundance changes of >1.5 or <0.67-fold were identified in BR007 and SC566, respectively. Protein interaction and pathway analyses indicated that proteins involved in the antioxidant system were more abundant in the tolerant line than in the sensitive one after Al treatment, while opposite trends were observed for proteins involved in lignin biosynthesis. Higher levels of ROS accumulation in root tips of the sensitive line due to decreased activity of antioxidant enzymes could lead to higher lignin production and hyper-accumulation of toxic Al in cell walls. These results indicated that activities of peroxidases and the balance between production and consumption of ROS could be important for Al tolerance and lignin biosynthesis in sorghum. [ABSTRACT FROM AUTHOR]

The Zn/Cd hyperaccumulator, Noccaea caerulescens, has been studied extensively for its ability to accumulate high levels of Zn and Cd in its leaves. Previous studies have indicated that the Zn and Cd hyperaccumulation trait exhibited by this species involves different transport and tolerance mechanisms. It has also been well documented that certain ecotypes of N. caerulescens are much better Cd hyperaccumulators than others. However, there does not seem to be much ecotypic variation for Zn hyperaccumulation in N. caerulescens. In this study we employed a comparative transcriptomics approach to look at root and shoot gene expression in Ganges and Prayon plants in response to Cd stress to identify transporter genes that were more highly expressed in either the roots or shoots of the superior Cd accumulator, Ganges. Comparison of the transcriptomes from the two ecotypes of Noccaea caerulescens identified a number of genes that encoded metal transporters that were more highly expressed in the Ganges ecotype in response to Cd stress. Characterization of one of these transporters, NcNramp1, showed that it is involved in the influx of Cd across the endodermal plasma membrane and thus may play a key role in Cd flux into the stele and root-to-shoot Cd transport. NcNramp1 may be one of the main transporters involved in Cd hyperaccumulation in N. caerulescens and copy number variation appears to be the main reason for high NcNramp1 gene expression underlying the increased Cd accumulation in the Ganges ecotype. [ABSTRACT FROM AUTHOR]

ABSTRACT High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice ( Oryza sativa) and maize ( Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population. [ABSTRACT FROM AUTHOR]

Root system architecture (RSA) plays an important role in the acquisition of mineral nutrients. Nevertheless, RSA has seldom been selected as an important agricultural trait in conventional breeding programs. Little is known about the response of RSA and phosphorus use efficiency (PUE) in regards to phosphorus (P) availability between parental inbred lines and their F1. In this study, 6 maize inbred lines and their 15 F1 generated by a diallel mating system, were used to analyze the genetic associations between RSA and PUE. Heterosis for PUE-related traits were comparatively greater under high P condition and reduced significantly under low P condition. Relative mid-parent heterosis for root traits were expressed more under the low P condition. Low P supply had a significant effect on heterosis, GCA and SCA of RSA- and PUE- related traits. The hybrid C3 (7922 × 8703-2), which had the highest PUE, showed an average yield with a lower P uptake under the both P conditions. Results from this study suggested breeding for a relatively high grain yield with reducing aboveground P demand and grain P concentration should be sufficient to reduce P fertilizer input and improve P efficiency. [ABSTRACT FROM AUTHOR]

A plant's ability to maintain or improve its yield under limiting conditions, such as nutrient deficiency or drought, can be strongly influenced by root system architecture (RSA), the three-dimensional distribution of the different root types in the soil. The ability to image, track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system, while allowing for aeration, solution replenishment and the imposition of nutrient treatments, as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modifications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity (detection of fine roots and other root details), higher efficiency, and a broad array of growing conditions for plants that more closely mimic those found under field conditions., (© 2015 Institute of Botany, Chinese Academy of Sciences.)